Re: [AMBER] variety of errors in membrane/umbrella sampling simulations

From: Baker, Joseph <>
Date: Sun, 29 Apr 2018 20:39:55 -0400

Dear Dave and others,

In fact one of our membrane dimensions is near 30 angstroms and when I ran
this with Amber18 just now I receive the following message immediately (for
a window in which we see the pairlist error)

Starting . Sun Apr 29 17:15:23 EDT 2018
gpu_neighbor_list_setup :: Small box detected, with <= 2 cells in one or
                           dimensions. The current GPU code has been deemed
                           unsafe for these situations. Please alter the
                           cutoff to increase the number of hash cells, make
                           use of the CPU code, or (if absolutely necessary)
                           run pmemd.cuda with the -AllowSmallBox flag.
                           behavior will be corrected in a forthcoming

We started the whole series of simulations with a pure POPE membrane
generated in charmm-gui with dimensions (x y z)
62.3850 62.1530 100.0000

Then we ran that for ~ 130 ns to equilibrate it. That ended up with
dimensions of
86.6804 40.0110 101.4163

We then went through a protocol to embed our small molecule in the bilayer,
used some steered MD to pull it out along z and -z to generate umbrella
windows, etc. One of our failed windows had a starting box dimension of
84.1245 41.7989 99.9944

Then at the end of the first 50 ns of umbrella simulation (which ran fine)
we had a box dimension of
103.2672 34.4123 99.2620

So the area stayed pretty constant in xy (3516 A^2 at beginning of umbrella
window, and 3554 A^2, so just about a 1% change)

When we then started the next 50 ns of simulation, the last frame printed
in this particular example (we were printing coordinates every 10 ps)
before the failure had a box size of
106.1403 34.8406 95.4016

So it appears that one of our box dimensions is continuing to sit pretty
close to this problematic system size that you mention. We are getting all
of these box size values using the cpptraj vector box out command.

Is the only way around this to reboot the simulations starting from larger
membranes (we have been using 64 lipids per monolayer)?

Kind regards,

Joseph Baker, PhD
Assistant Professor
Department of Chemistry
C101 Science Complex
The College of New Jersey
Ewing, NJ 08628
Phone: (609) 771-3173

On Sun, Apr 29, 2018 at 5:00 PM, David A Case <>

> On Sat, Apr 28, 2018, Baker, Joseph wrote:
> >
> > (3) ERROR: max pairlist cutoff must be less than unit cell max sphere
> > radius!
> How big is your simulation box? We recently discovered that pmemd.cuda
> can crash with large forces when run on small systems (with a dimension
> less than roughly 30 Ang -- sorry, I don't have exact details
> available.)
> > I should also add that at our site we have spot-checked one of the
> failing
> > windows by continuing it on the CPU instead of the GPU for the 2nd 50 ns,
> > and that works fine as well. So it appears that problems arise in only
> some
> > windows and only when trying to run the second 50 ns of these simulations
> > on a GPU device.
> Above would be consistent with my speculation. Try running a short
> simulation using the Amber18 code. That will tell you if your system is
> susceptible to this particular problem, by exiting with an informative
> error message.
> ...regards...dac
> cc-ing to Dave Cerutti: independent of this particular users' problem,
> we need to the get the small system check back-ported to Amber16.
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Received on Sun Apr 29 2018 - 18:00:02 PDT
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